ENH: Cleanup comments and inheritance syntax a bit. Remove unnecessary...

ENH: Cleanup comments and inheritance syntax a bit.  Remove unnecessary Geometry Types not needed since splitting structured and unstructured grids
into separate hierarchies.

XdmfGeometryType.cpp

@@ -26,30 +26,6 @@ boost::shared_ptr<const XdmfGeometryType> XdmfGeometryType::XY()
 	return p;
 }
 
-boost::shared_ptr<const XdmfGeometryType> XdmfGeometryType::X_Y_Z()
-{
-	static boost::shared_ptr<const XdmfGeometryType> p(new XdmfGeometryType("X_Y_Z", 3));
-	return p;
-}
-
-boost::shared_ptr<const XdmfGeometryType> XdmfGeometryType::X_Y()
-{
-	static boost::shared_ptr<const XdmfGeometryType> p(new XdmfGeometryType("X_Y", 2));
-	return p;
-}
-
-boost::shared_ptr<const XdmfGeometryType> XdmfGeometryType::VXVYVZ()
-{
-	static boost::shared_ptr<const XdmfGeometryType> p(new XdmfGeometryType("VXVYVZ", 3));
-	return p;
-}
-
-boost::shared_ptr<const XdmfGeometryType> XdmfGeometryType::VXVY()
-{
-	static boost::shared_ptr<const XdmfGeometryType> p(new XdmfGeometryType("VXVY", 2));
-	return p;
-}
-
 XdmfGeometryType::XdmfGeometryType(const std::string& name, const int& dimensions) :
 	mDimensions(dimensions),
 	mName(name)
@@ -83,22 +59,6 @@ boost::shared_ptr<const XdmfGeometryType> XdmfGeometryType::New(const std::map<s
 		{
 			return XY();
 		}
-		else if(typeVal.compare("X_Y_Z") == 0)
-		{
-			return X_Y_Z();
-		}
-		else if(typeVal.compare("X_Y") == 0)
-		{
-			return X_Y();
-		}
-		else if(typeVal.compare("VXVYVZ") == 0)
-		{
-			return VXVYVZ();
-		}
-		else if(typeVal.compare("VXVY") == 0)
-		{
-			return VXVY();
-		}
 		else
 		{
 			assert(false);

XdmfGeometryType.hpp

@@ -15,12 +15,6 @@
  * 	NoGeometryType
  * 	XYZ
  * 	XY
- * 	X_Y_Z
- * 	X_Y
- * 	VXVYVZ
- * 	Origin_DXDYDZ
- * 	VXVY
- * 	Origin_DXDY
  */
 class XdmfGeometryType : public XdmfItemProperty {
 
@@ -34,10 +28,6 @@ public:
 	static boost::shared_ptr<const XdmfGeometryType> NoGeometryType();
 	static boost::shared_ptr<const XdmfGeometryType> XYZ();
 	static boost::shared_ptr<const XdmfGeometryType> XY();
-	static boost::shared_ptr<const XdmfGeometryType> X_Y_Z();
-	static boost::shared_ptr<const XdmfGeometryType> X_Y();
-	static boost::shared_ptr<const XdmfGeometryType> VXVYVZ();
-	static boost::shared_ptr<const XdmfGeometryType> VXVY();
 
 	/**
 	 * Get the dimensions of this geometry type - i.e. XYZ = 3.

XdmfGrid.cpp

@@ -16,9 +16,9 @@
 XDMF_CHILDREN_IMPLEMENTATION(XdmfGrid, XdmfAttribute, Attribute, Name)
 XDMF_CHILDREN_IMPLEMENTATION(XdmfGrid, XdmfSet, Set, Name)
 
-XdmfGrid::XdmfGrid(const std::string & name) :
-	mGeometry(XdmfGeometry::New()),
-	mTopology(XdmfTopology::New()),
+XdmfGrid::XdmfGrid(const boost::shared_ptr<XdmfGeometry> geometry, const boost::shared_ptr<XdmfTopology> topology, const std::string & name) :
+	mGeometry(geometry),
+	mTopology(topology),
 	mMap(boost::shared_ptr<XdmfMap>()),
 	mName(name),
 	mTime(boost::shared_ptr<XdmfTime>())

XdmfGrid.hpp

@@ -19,6 +19,8 @@ class XdmfTopology;
  * that stores point locations and an XdmfTopology that store connectivity information.  XdmfAttributes can be inserted
  * into the XdmfGrid to specify fields centered on various parts of the mesh.  XdmfSets can be inserted into XdmfGrids
  * to specify collections of mesh elements.
+ *
+ * XdmfGrid is an abstract base class.  There are several implementations for representing both structured and unstructured grids.
  */
 class XdmfGrid : public virtual XdmfItem {
 
@@ -111,7 +113,8 @@ public:
 
 protected:
 
-	XdmfGrid(const std::string & name = "Grid");
+	XdmfGrid(const boost::shared_ptr<XdmfGeometry> geometry, const boost::shared_ptr<XdmfTopology> topology, const std::string & name = "Grid");
+
 	virtual void populateItem(const std::map<std::string, std::string> & itemProperties, std::vector<boost::shared_ptr<XdmfItem> > & childItems, const XdmfCoreReader * const reader);
 
 	boost::shared_ptr<XdmfGeometry> mGeometry;

XdmfGridCollection.cpp

@@ -5,6 +5,8 @@
  *      Author: kleiter
  */
 
+#include "XdmfGeometry.hpp"
+#include "XdmfTopology.hpp"
 #include "XdmfGridCollection.hpp"
 #include "XdmfGridCollectionType.hpp"
 
@@ -16,7 +18,7 @@ boost::shared_ptr<XdmfGridCollection> XdmfGridCollection::New()
 
 XdmfGridCollection::XdmfGridCollection() :
 	XdmfDomain(),
-	XdmfGrid("Collection"),
+	XdmfGrid(XdmfGeometry::New(), XdmfTopology::New(), "Collection"),
 	mType(XdmfGridCollectionType::NoCollectionType())
 {
 }

XdmfGridCurvilinear.cpp

@@ -7,6 +7,7 @@
 
 #include <cmath>
 #include "XdmfArray.hpp"
+#include "XdmfGeometry.hpp"
 #include "XdmfGridCurvilinear.hpp"
 #include "XdmfTopology.hpp"
 #include "XdmfTopologyType.hpp"
@@ -141,9 +142,9 @@ boost::shared_ptr<XdmfGridCurvilinear> XdmfGridCurvilinear::New(const boost::sha
 }
 
 XdmfGridCurvilinear::XdmfGridCurvilinear(const boost::shared_ptr<XdmfArray> numPoints) :
+	XdmfGrid(XdmfGeometry::New(), XdmfGridCurvilinearImpl::XdmfTopologyCurvilinear::New(this)),
 	mImpl(new XdmfGridCurvilinearImpl(numPoints))
 {
-	mTopology = XdmfGridCurvilinearImpl::XdmfTopologyCurvilinear::New(this);
 }
 
 XdmfGridCurvilinear::~XdmfGridCurvilinear()

XdmfGridRectilinear.cpp

@@ -235,10 +235,9 @@ boost::shared_ptr<XdmfGridRectilinear> XdmfGridRectilinear::New(const std::vecto
 }
 
 XdmfGridRectilinear::XdmfGridRectilinear(const std::vector<boost::shared_ptr<XdmfArray> > & axesCoordinates) :
+	XdmfGrid(XdmfGridRectilinearImpl::XdmfGeometryRectilinear::New(this), XdmfGridRectilinearImpl::XdmfTopologyRectilinear::New(this)),
 	mImpl(new XdmfGridRectilinearImpl(axesCoordinates))
 {
-	mGeometry = XdmfGridRectilinearImpl::XdmfGeometryRectilinear::New(this);
-	mTopology = XdmfGridRectilinearImpl::XdmfTopologyRectilinear::New(this);
 }
 
 XdmfGridRectilinear::~XdmfGridRectilinear()

XdmfGridRegular.cpp

@@ -259,10 +259,9 @@ boost::shared_ptr<XdmfGridRegular> XdmfGridRegular::New(const boost::shared_ptr<
 
 XdmfGridRegular::XdmfGridRegular(const boost::shared_ptr<XdmfArray> brickSize, const boost::shared_ptr<XdmfArray> numPoints,
 	const boost::shared_ptr<XdmfArray> origin) :
+	XdmfGrid(XdmfGridRegularImpl::XdmfGeometryRegular::New(this), XdmfGridRegularImpl::XdmfTopologyRegular::New(this)),
 	mImpl(new XdmfGridRegularImpl(brickSize, numPoints, origin))
 {
-	mGeometry = XdmfGridRegularImpl::XdmfGeometryRegular::New(this);
-	mTopology = XdmfGridRegularImpl::XdmfTopologyRegular::New(this);
 }
 
 XdmfGridRegular::~XdmfGridRegular()

XdmfGridUnstructured.cpp

@@ -5,7 +5,9 @@
  *      Author: kleiter
  */
 
+#include "XdmfGeometry.hpp"
 #include "XdmfGridUnstructured.hpp"
+#include "XdmfTopology.hpp"
 
 boost::shared_ptr<XdmfGridUnstructured> XdmfGridUnstructured::New()
 {
@@ -14,7 +16,7 @@ boost::shared_ptr<XdmfGridUnstructured> XdmfGridUnstructured::New()
 }
 
 XdmfGridUnstructured::XdmfGridUnstructured() :
-	XdmfGrid()
+	XdmfGrid(XdmfGeometry::New(), XdmfTopology::New())
 {
 }
 

XdmfGridUnstructured.hpp

@@ -5,12 +5,11 @@
 #include "XdmfGrid.hpp"
 
 /**
- * @brief A mesh containing elements, points, and fields attached to the mesh.
+ * @brief An unstructured grid consisting of elements, points, and fields attached to the mesh.
  *
- * XdmfGrid represents a mesh.  It is required to contain two other Xdmf data structures, an XdmfGeometry
- * that stores point locations and an XdmfTopology that store connectivity information.  XdmfAttributes can be inserted
- * into the XdmfGrid to specify fields centered on various parts of the mesh.  XdmfSets can be inserted into XdmfGrids
- * to specify collections of mesh elements.
+ * After creating an unstructured grid, the XdmfGeometry and XdmfTopology must be set.  The XdmfTopology
+ * describes the element types contained in the grid and their connectivity.  The XdmfGeometry describes the
+ * location of nodes.
  */
 class XdmfGridUnstructured : public XdmfGrid {
 

XdmfTopologyType.hpp

@@ -36,12 +36,6 @@
  * 	Hexahedron_125 - 125 Node Tri-Quartic Hexahedron
  * 	Hexahedron_125_GLL - 125 Node Spectral Tri-Quartic Hexahedron with Gauss-Lobatto-Legendre points.
  * 	Mixed - Mixture of Unstructured Topologies
- * 	TwoDSMesh
- * 	TwoDRectMesh
- * 	TwoDCoRectMesh
- * 	ThreeDSMesh
- * 	ThreeDRectMesh
- * 	ThreeDCoRectMesh
  */
 class XdmfTopologyType : public XdmfItemProperty {
 

core/XdmfCoreReader.hpp

@@ -15,6 +15,8 @@ class XdmfItem;
  *
  * Reads an Xdmf structured file stored on disk into an Xdmf structure in memory.  All light data is parsed in order to create appropriate
  * Xdmf objects.  Heavy data controllers are created and attached to XdmfArrays but no heavy data is read into memory.
+ *
+ * XdmfCoreReader is an abstract base class.
  */
 class XdmfCoreReader {
 

utils/XdmfExodusWriter.cpp

@@ -146,25 +146,13 @@ void XdmfExodusWriter::write(const std::string & filePath, const boost::shared_p
 	double * y = new double[num_nodes];
 	double * z = new double[num_nodes];
 	// Write nodal coordinate values to exodus
-	if(currGrid->getGeometry()->getType() == XdmfGeometryType::XYZ() || currGrid->getGeometry()->getType() == XdmfGeometryType::XY())
+	currGrid->getGeometry()->getValues(0, x, num_nodes, 3);
+	currGrid->getGeometry()->getValues(1, y, num_nodes, 3);
+	if(currGrid->getGeometry()->getType() == XdmfGeometryType::XYZ())
 	{
-		currGrid->getGeometry()->getValues(0, x, num_nodes, 3);
-		currGrid->getGeometry()->getValues(1, y, num_nodes, 3);
-		if(currGrid->getGeometry()->getType() == XdmfGeometryType::XYZ())
-		{
-			currGrid->getGeometry()->getValues(2, z, num_nodes, 3);
-		}
-		ex_put_coord(exodusHandle, x ,y ,z);
-	}
-	else if(currGrid->getGeometry()->getType() == XdmfGeometryType::X_Y_Z() || currGrid->getGeometry()->getType() == XdmfGeometryType::X_Y())
-	{
-		currGrid->getGeometry()->getValues(0, x, num_nodes);
-		currGrid->getGeometry()->getValues(num_nodes, y, num_nodes);
-		if(currGrid->getGeometry()->getType() == XdmfGeometryType::X_Y_Z())
-		{
-			currGrid->getGeometry()->getValues(num_nodes * 2, z, num_nodes);
-		}
+		currGrid->getGeometry()->getValues(2, z, num_nodes, 3);
 	}
+	ex_put_coord(exodusHandle, x ,y ,z);
 	delete [] x;
 	delete [] y;
 	delete [] z;